[gmx-users] (no subject)
Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 7 01:59:59 CEST 2011
Sai Janani Ganesan wrote:
> Thanks for the reply!
> I tried the rates, and only the terminal with positive rate gets pulled.
> The first and the last amino acids are spatially oriented one behind the
> other. I think defining a vector might work better, but I am not sure
> why nothing happens when I define a pull_vec1 and pull_vec2. Am I
> missing anything?
When setting "distance" as the pull_geometry, only pull_dim is used; pull_vec is
ignored. If you want to define vectors, use the "direction" pull_geometry.
> On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> Sai Janani Ganesan wrote:
> I am trying to pull the first from the last amino acid of a
> protein to completely unfold the protein in the X direction. I
> chose the middle amino acid as the reference, and the groups get
> pulled in the same direction or opposite direction (which is
> what I want) depending on the trial. I am trying to find a
> definite method to completely unfold it.
> I define a different vector (pull_vec1 and pull_vec2) with +x
> and -x values and that does not even pull the protein
> I tried using only pull_group1 and pull_group2, without a
> reference, and neither groups get pulled.
> I chose different references, I do have some success but I don't
> think it is the best way to do it.
> How do I pull the N and C terminal apart, by simultaneously
> pulling them in opposite directions?Why is my vector definition
> This is my pull code:
> pull = umbrella
> pull_geometry = distance
> pull_dim = Y N N
> pull_start = yes pull_ngroups = 2
> pull_group0 = Chain-C
> pull_group1 = Chain-B
> pull_group2 = Chain-A
> %pull_vec1 = -31 0 0
> %pull_vec2 = 31 0 0
> I suspect the % signs will mess things up, but probably will give a
> fatal error, if nothing else.
> pull_rate1 = 0.002 pull_k1 = 1000 pull_rate2
> = 0.002 pull_k2 = 1000
> Here's the problem. You're telling the two pulled groups to move in
> the same direction. With "distance" geometry, the selections are a
> bit more simplistic. If you set pull_rate1 to -0.002 and pull_rate2
> to 0.002, the groups will be pulled in opposite directions.
> Otherwise, you're just towing your protein along in the box.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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